Simple opacity material in cycles?
Now I feel dumb because I just realised how you can do this after posting the question.. :P
Anyways, here's one way to do it:

It's actually really simple node setup. You just have to combine a diffuse/transparent mix with a fully transparent node, and use transparency depth as a factor.



That way cycles disregards anything that is behind the first "layer" of transparency. Here's the result:



It's a much cleaner and nicer opacity-like transparency for many cases. I'll use it for illustrative/instructional animations and motion graphics, since those are all areas where simplicity is very important and transparent materials are often needed.

And best of all, you are saved from setting up different renderlayers and compositing nodes, and it also reduces rendertimes in many cases because there's no need for multiple renders!